Approximate Profile Maximum Likelihood

We propose an efficient algorithm for approximate computation of the profile maximum likelihood (PML), a variant of maximum likelihood maximizing the probability of observing a sufficient statistic rather than the empirical sample. The PML has appealing theoretical properties, but is difficult to compute exactly. Inspired by observations gleaned from exactly solvable cases, we look for an approximate PML solution, which, intuitively, clumps comparably frequent symbols into one symbol. This amounts to lower-bounding a certain matrix permanent by summing over a subgroup of the symmetric group rather than the whole group during the computation. We extensively experiment with the approximate solution, and find the empirical performance of our approach is competitive and sometimes significantly better than state-of-the-art performance for various estimation problems

Phylogenetic tree based on maximum-parsimony (MP) and maximum-likelihood (ML) analyses depicting the relationship among the pyrotags affiliated with <i>Bacteroidetes</i>.

<p>Reference OTU from <i>Cryptocercus</i> and <i>Parasphaeria</i> were in bold. Other references OTU were obtained from <i>Cryptocercus</i> CP-1, CP-2 and CP-3 (Bioproject PRJNA238270), <i>Reticulitermes grassei</i> [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0152400#pone.0152400.ref068" target="_blank">68</a>], <i>Blattella germanica</i> (Bioproject PRJEB3414) and <i>Pyrrhcoris apterus</i> (firebug) Bioproject PRJNA171139. In parentheses, the number of OTUs found repeatedly (at 0.10% genetic distance level). One thousand bootstrap trees were generated; bootstrap confidence levels, as percentages (only values >50%), are shown at tree nodes.</p

Venn diagram.

<p><i>Parasphaeria</i> and <i>Cryptocercus</i> shared 6 OUT at 0.10 distances. Figure showed the two cockroaches. (Photo by M. Berlanga and R. Duro).</p

Gut Bacterial Community of the Xylophagous Cockroaches <i>Cryptocercus punctulatus</i> and <i>Parasphaeria boleiriana</i>

<div><p><i>Cryptocercus punctulatus</i> and <i>Parasphaeria boleiriana</i> are two distantly related xylophagous and subsocial cockroaches. <i>Cryptocercus</i> is related to termites. Xylophagous cockroaches and termites are excellent model organisms for studying the symbiotic relationship between the insect and their microbiota. In this study, high-throughput 454 pyrosequencing of 16S rRNA was used to investigate the diversity of metagenomic gut communities of <i>C</i>. <i>punctulatus</i> and <i>P</i>. <i>boleiriana</i>, and thereby to identify possible shifts in symbiont allegiances during cockroaches evolution. Our results revealed that the hindgut prokaryotic communities of both xylophagous cockroaches are dominated by members of four <i>Bacteria</i> phyla: <i>Bacteroidetes</i>, <i>Firmicutes</i>, <i>Proteobacteria</i>, and <i>Actinobacteria</i>. Other identified phyla were <i>Spirochaetes</i>, <i>Planctomycetes</i>, <i>candidatus</i> Saccharibacteria (formerly TM7), and <i>Acidobacteria</i>, each of which represented 1–2% of the total population detected. Community similarity based on phylogenetic relatedness by unweighted UniFrac analyses indicated that the composition of the bacterial community in the two species was significantly different (<i>P</i> < 0.05). Phylogenetic analysis based on the characterized clusters of <i>Bacteroidetes</i>, <i>Spirochaetes</i>, and <i>Deltaproteobacteria</i> showed that many OTUs present in both cockroach species clustered with sequences previously described in termites and other cockroaches, but not with those from other animals or environments. These results suggest that, during their evolution, those cockroaches conserved several bacterial communities from the microbiota of a common ancestor. The ecological stability of those microbial communities may imply the important functional role for the survival of the host of providing nutrients in appropriate quantities and balance.</p></div

Phylogenetic tree based on maximum-parsimony (MP) and maximum-likelihood (ML) analyses depicting the relationship among the pyrotags affiliated with the <i>Treponema</i> I, II, and III clades in termites and cockroaches.

<p>Reference OTU from <i>Cryptocercus</i> and <i>Parasphaeria</i> were in bold. Other references OTU were obtained from <i>Cryptocercus</i> CP-1, CP-2 and CP-3 (Bioproject PRJNA238270) and <i>Reticulitermes grassei</i> [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0152400#pone.0152400.ref068" target="_blank">68</a>]. In parentheses, the number of OTUs found repeatedly (at 0.05% genetic distance level). One thousand bootstrap trees were generated; bootstrap confidence levels, as percentages (only values >50%), are shown at tree nodes.</p

Main assembly summary and annotation features of the three <i>F. avenaceum</i> genomes.

<p>*Post- removal of mitochondrial genome.</p><p>Main assembly summary and annotation features of the three <i>F. avenaceum</i> genomes.</p

Metabolic profiling of the three <i>F. avenaceum</i> strains.

<p>Metabolic profiling of the three <i>F. avenaceum</i> strains.</p

Functional analysis of Fa05001 and other sequenced Fusaria based on InterPro visualizing similarities and differences between the fungi.

<p>Categories with most differences between Fa05001 and others are presented with the number of proteins in each category. All details are listed in File S4. FA  =  <i>F. avenaceum</i> Fa05001, FG  =  <i>F. graminearum</i> PH-1, FO <i> =  F. oxysporum</i> f. sp. <i>lycopersici</i> 4287, FV  =  <i>F. verticillioides,</i> FS  =  <i>F. solani.</i></p

Molecular phylogenetic analysis of Fusarium species based on 69 orthologous proteins.

<p>The evolutionary history was inferred by using the Maximum Likelihood method and the tree with the highest log likelihood (−152577,9625) is shown. Bootstrap values, as percentages, are shown next to the individual branches. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. All positions containing gaps and missing data were eliminated prior to the ML analysis and the final data set contained 25535 positions.</p

InterproScan analysis and comparison of Fa05001 with other Fusaria.

<p>InterproScan analysis and comparison of Fa05001 with other Fusaria.</p